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- EMDB-38912: Overall map of PSII-CAC -

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Basic information

Entry
Database: EMDB / ID: EMD-38912
TitleOverall map of PSII-CAC
Map dataOverall map of PSII-CAC from Rhodomonas salina
Sample
  • Complex: Inactive Photosystem II associated with chlorophyll a/c binding protein
KeywordsPhotosystem II associated with CAC antenna from Rhodomonas Salina / PHOTOSYNTHESIS
Biological speciesRhodomonas salina (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsSi L / Li M
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for the distinct core-antenna assembly of cryptophyte photosystem II
Authors: Si L / Zhang S / Su X / Li M
History
DepositionJan 30, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38912.png

Downloads & links

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Map

FileDownload / File: emd_38912.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall map of PSII-CAC from Rhodomonas salina
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 416 pix.
= 432.653 Å		1.04 Å/pix.
x 416 pix.
= 432.653 Å		1.04 Å/pix.
x 416 pix.
= 432.653 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04003 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0281
Minimum - Maximum-0.102093 - 0.2220462
Average (Standard dev.)0.00014272142 (±0.0061794585)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 432.65326 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38912_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38912_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Inactive Photosystem II associated with chlorophyll a/c binding p...

EntireName: Inactive Photosystem II associated with chlorophyll a/c binding protein
Components
  • Complex: Inactive Photosystem II associated with chlorophyll a/c binding protein

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Supramolecule #1: Inactive Photosystem II associated with chlorophyll a/c binding p...

SupramoleculeName: Inactive Photosystem II associated with chlorophyll a/c binding protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17, #19-#24
Source (natural)Organism: Rhodomonas salina (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6jlu

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 112613
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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